Matrix metalloproteinase



Matrix metalloproteinases (MMP) are Zinc-dependent endopeptidases. MMP degrades extracellular matrix proteins. MMPs are produced by 28 different genes and are classified according to their protein substrates. They are inhibited by proteases called tissue inhibitors of metalloproteinase (TIMP). The pro-MMP contains a pro-peptide which must be removed to render the MMP active. The images at the left and at the right correspond to one representative MMP, i.e. the crystal structure of human pro MMP1 (1su3).

MT1-MMP-TIMP-1 complex


The human matrix metalloproteinases (MMPs) family comprises a large group of structurally homologous zinc-dependent endopeptidases (e.g. membrane type-1 matrix metalloproteinase (MT1-MMP) (darkmagenta) and membrane type-3 matrix metalloproteinase (MT3-MMP) (magenta), click to see structural comparison ) that perform a wide variety of biological roles. In general, the MMPs are inhibited unselectively by all four known tissue inhibitors of metalloproteinases (TIMPs 1-4) which have 40-50% sequence identity. For example, membrane type-3 matrix metalloproteinase (MT3-MMP) can form complex with wild-type TIMP-1 (1uea, colored orange ). The WT-TIMP-1 binding interface (cyan) is mainly composed of the N-terminal segment that approaches the active site, the AB loop (Thr33-Tyr35), the CD loop (Ala65-Cys70), and the EF loop (Thr97-Ser100). The pivotal residue, threonine 98 (Thr98), is shown as red sticks. In general, five main chain hydrogen bonds (Cys1-Ser68, Val69-Met66, Gly71-Met66, Cys70-Glu67, and Cys70-Thr98) are intimately involved in the conformational stability of TIMP binding interface when bound to MMP. Membrane type-1 matrix metalloproteinase (MT1-MMP) (darkmagenta) also forms complex with wild-type TIMP-1 (2j0t, <font color='orange'>colored orange ), producing <scene name='MT1-MMP-TIMP-1_complex/Cv2/12'>similar hydrogen bond network in the WT TIMP-1 binding interface as well as <scene name='MT1-MMP-TIMP-1_complex/Cv2/13'>in the case with MT3-MMP. This network of hydrogen bonds stabilizes the CD and EF loops that compose the binding interface. Importantly, the <scene name='MT1-MMP-TIMP-1_complex/Cv2/14'>hydrogen bond between Cys1 and Ser68 may position the amino and carboxyl groups of Cys1 to effectively coordinate the Zn2+ ion. However, this MT1-MMP-WT-TIMP-1 complex is not tight-binding. MT1-MMP is unique since even though it exhibits high structural homology to all MMPs, it is not inhibited by TIMP-1, <scene name='MT1-MMP-TIMP-1_complex/Cv3/1'>but is inhibited by the structural homologous TIMP-2 (1bqq). <scene name='MT1-MMP-TIMP-1_complex/Cv2/15'>The single point mutation T98L (mutant TIMP-1 is colored in yellow with <font color='red'>T98L shown in red ) transformed TIMP-1 into a high affinity inhibitor of MT1-MMP (3ma2). WT-TIMP-1, WT-TIMP-2, and TIMP-1 T98L mutant have kinetic dissociation binding constant (KD) 1.53 x 10-6, 5.61 x 10-8, and 8.70 x 10-8, respectively. So, KD of WT-TIMP-2 is 2 orders of magnitude smaller than that of WT-TIMP-1, indicating the weak affinity between MT1-MMP and WT-TIMP-1. The TIMP-1 T98L mutant regained high-affinity binding to MT1-MMP, resulting in a 2 order of magnitude decrease in KD, similar to the case for WT-TIMP-2, the in vivo inhibitor of MT1-MMP. The overall structures of the complexes of <font color='darkmagenta'>MT1-MMP -<font color='orange'>WT-TIMP-1 and <font color='violet'>MT1-MMP - mutant-T98L-TIMP-1 are <scene name='MT1-MMP-TIMP-1_complex/Cv2/17'>relatively similar. Even the structure of <font color='magenta'>MT3-MMP -<font color='orange'>WT-TIMP-1 is <scene name='MT1-MMP-TIMP-1_complex/Cv2/18'>similar to those of MT1-MMP-TIMP-1s (with <font color='orange'>wild-type and TIMP-1 T98L mutant ). <scene name='MT1-MMP-TIMP-1_complex/Cv4/1'>Leu98 is pointing toward MT1-MMP residues Pro259 and Phe260, establishing a strong hydrophobic core, which is situated near the MT1-MMP <scene name='MT1-MMP-TIMP-1_complex/Cv4/3'>catalytic Zn2+ ion surrounded by His239, His243, and His249. So, this T98L replacement may stabilize the entire area by establishing a strong hydrophobic core upon binding to the enzyme. However, it seems unlikely that these additional bonds could account for the entire binding effect between MT1-MMP and TIMP-1. Statistical analysis of the <scene name='MT1-MMP-TIMP-1_complex/Cv2/15'>key hydrogen bond stabilities in the TIMP-1 T98L mutant reveals that the hydrogen bonds network in mutant form is significantly more stable than that in WT-TIMP-1. Mutations that enhance hydrogen bond stability contribute to the stability of the bound-like, less flexible, conformation of TIMP-1, which eventually results in increasing binding affinity for MT1-MMP. Thus, mutation affected the instrinsic dynamics of the inhibitor rather than its structure, thereby facilitating the interaction.

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MMP1 interstitial collagenase
1su3 – pro-hMMP – human

MMP2 gelatinase-A
1qib - hMMP catalytic domain (mutant) <BR /> 1rtg - hMMP hemopexin-like domain<BR /> 1ks0 – hMMP first fibronectin type II domain – NMR<BR /> 1cxw - hMMP second fibronectin type II domain – NMR<BR /> 1j7m - hMMP third fibronectin type II domain (mutant) – NMR<BR /> 1eak – pro-hMMP catalytic domain (mutant) + peptide inhibitor

1hov, 1eub - hMMP catalytic domain + inhibitor– NMR<BR /> 1gxd – pro-hMMP (mutant) + TIMP-2

MMP3 stromelysin 1
1qia, 1qic, 1cqr, 1slm - hMMP catalytic domain<BR /> 3ohl, 3oho, 1g49, 1ciz, 1b8y, 1caq, 1usn, 2usn, 1ums, 1umt – hMMP catalytic domain + inhibitor

1uea - hMMP catalytic domain + TIMP-1<BR /> 1oo9 - hMMP catalytic domain + TIMP-1 N terminal<BR /> 2jt5, 2jt6, 2jnp, 3usn, 1sln - hMMP catalytic domain + inhibitor – NMR<BR />

MMP7 matrilysin
2y6c, 2y6d – hMMP residues 95-298 + inhibitor

MMP8 neutrophil collagenase
3dng, 3dpe, 3dpf, 1zp5, 1jh1, 1jj9, 1i76, 1a85, 1mmb – hMMP catalytic domain + inhibitor

1i73 - hMMP catalytic domain + peptide inhibitor

MMP9 gelatinase-B
1l6j - pro-hMMP<BR /> 1gkc - hMMP catalytic domain + inhibitor

2ovx, 2ovz, 2ow0, 2ow1, 2ow2, 1gkd - hMMP catalytic domain (mutant) + inhibitor

MMP10 stromelysin 2
1q3a - hMMP catalytic domain (mutant)

MMP11 stromelysin 3
1hv5 - hMMP catalytic domain + inhibitor

MMP12 macrophage
3ba0, 2oxu - hMMP<BR /> 2krj, 2k9c - hMMP catalytic domain – NMR<BR /> 1jk3 - hMMP catalytic domain <BR /> 2poj - hMMP catalytic domain (mutant) - NMR<BR /> 2jxy - hMMP hemopexin-like domain - NMR<BR /> 3n2u, 3n2v, 2wo8, 2wo9, 2woa, 1utt, 1utz, 1ros – hMMP catalytic domain + inhibitor

3lk8, 3lik, 3lil, 3lir, 3ljg, 3nx7, 3lka, 3ehx, 3ehy, 3f15, 3f16, 3f17, 3f18, 3f19, 3f1a, 1y93, 1rmz, 1os2, 1os9 - hMMP catalytic domain (mutant) + inhibitor

2k2g, 2z2d - hMMP catalytic domain + inhibitor - NMR<BR /> 2w0d, 1ycm, 1z3j - hMMP catalytic domain (mutant) + inhibitor - NMR<BR />

MMP13 collagenase 3
1cxv - MMP catalytic domain - mouse<BR /> 2yig, 3ljz, 3kec, 3kej, 3kek, 3kry, 3i7g, 3i7i, 3elm, 2pjt, 2ozr, 1xuc, 1xud, 1xur, 1you – hMMP catalytic domain + inhibitor

MMP14 Membrane T1
3ma2 – hMMP residues 112-292 + TIMP-1 (mutant) <BR /> 1buv, 1bqq - hMMP + TIMP-2<BR /> 3c7x – hMMP hemopexin-like domain

MMP16 Membrane T3
1rm8 - hMMP catalytic domain + inhibitor

MMP20 enamelysin
2jsd - hMMP catalytic domain + inhibitor - NMR<BR />

MMP23 CA-MMP
2k72 – hMMP residues 254-290 - NMR<BR />